Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 21ccf76b1009301365171d7a33afb380b40dd3a3
https://github.com/galaxyproject/galaxy/commit/21ccf76b1009301365171d7a33af…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-09-01 (Thu, 01 Sep 2016)
Changed paths:
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
API, history contents: contents download endpoint
- Adds an api endpoint at 'histories/{id}/contents/archive' for
creating an archive from all history contents or a filtered subset
of contents
- Contents are returned in 'tgz' format currently
- Datasets are located in the archive in paths roughly matching the
nesting relationships of their parent collections
- Filters can be applied using the same syntax as index
- Adding 'dry_run=True' will return a JSON list of archive paths and
dataset file paths for debugging
- Adds map_datasets method for walking the datasets of histories and
HDCAs
Commit: e76bbf53b62f29f2d05459ecea13fd8e98449aa4
https://github.com/galaxyproject/galaxy/commit/e76bbf53b62f29f2d05459ecea13…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #2885 from carlfeberhard/file-walker
API, history contents: contents download endpoint
Compare: https://github.com/galaxyproject/galaxy/compare/f553d387a47d...e76bbf53b62f
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: de763bedee23494035752c11abc5a62e26364e47
https://github.com/galaxyproject/galaxy/commit/de763bedee23494035752c11abc5…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-12 (Fri, 12 Aug 2016)
Changed paths:
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/tracks.js
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/tracks.js.map
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Initial commit to get working BBI reader into Trackster.
Commit: cdc82ef2f8d3f7c6c1f5e274fc5896f8e6e7aa48
https://github.com/galaxyproject/galaxy/commit/cdc82ef2f8d3f7c6c1f5e274fc58…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-19 (Fri, 19 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M client/galaxy/style/less/library.less
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/queues.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
A lib/galaxy/util/postfork.py
M lib/galaxy/util/template.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/proxy/js/lib/main.js
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/web/proxy/js/package.json
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/controllers/hg.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/galaxy_install/update_repository_manager.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/style/blue/base.css
M static/style/blue/library.css
M templates/webapps/galaxy/workflow/run.mako
M test/base/interactor.py
A test/functional/tools/dbkey_output_action.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/tool_provided_metadata_1.xml
A test/functional/tools/tool_provided_metadata_2.xml
A test/functional/tools/tool_provided_metadata_3.xml
Log Message:
-----------
Merge branch 'dev' into bbi-js3
Commit: d99cbd79b61005b90ec5871fd90cec113d0ed21e
https://github.com/galaxyproject/galaxy/commit/d99cbd79b61005b90ec5871fd90c…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M config/galaxy.ini.sample
M config/reports.ini.sample
M config/tool_shed.ini.sample
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/security/validate_user_input.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/util/postfork.py
M lib/galaxy/webapps/tool_shed/config.py
Log Message:
-----------
Merge branch 'dev' into bbi-js3
Commit: 41d0ee4f4392d188ec9ededa35391ef592213608
https://github.com/galaxyproject/galaxy/commit/41d0ee4f4392d188ec9ededa3539…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-23 (Tue, 23 Aug 2016)
Changed paths:
M client/galaxy/scripts/libs/bbi/bigwig.js
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M static/maps/libs/bbi/bigwig.js.map
M static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/libs/bbi/bigwig.js
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Bring data provided by data manager in line with Trackster's bigwig datatype. Also allow LinePainter to draw regions of variable length.
Commit: 74be6955b3c73feb5db6fc2ee0c66179672f8a6f
https://github.com/galaxyproject/galaxy/commit/74be6955b3c73feb5db6fc2ee0c6…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-24 (Wed, 24 Aug 2016)
Changed paths:
M client/galaxy/scripts/viz/trackster/tracks.js
M static/maps/viz/trackster/tracks.js.map
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Detect whether server has byte-range support and set LineTrack data manager appropriately.
Commit: 7b44cc5470728b59a2b47c64aedd27774706dd8b
https://github.com/galaxyproject/galaxy/commit/7b44cc5470728b59a2b47c64aedd…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M .ci/flake8_lint_include_list.txt
M Makefile
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/utils/utils.js
M config/galaxy.ini.sample
M config/plugins/visualizations/charts/static/app.css
M config/plugins/visualizations/charts/static/app.js
R config/plugins/visualizations/charts/static/charts/forms/default.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/plot-config.js
M config/plugins/visualizations/charts/static/charts/jqplot/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/config.js
M config/plugins/visualizations/charts/static/charts/jqplot/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_horizontal_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/bar_stacked/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/common/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/histogram_discrete/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/line_focus/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/scatter/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_full/wrapper.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/config.js
M config/plugins/visualizations/charts/static/charts/nvd3/stackedarea_stream/wrapper.js
A config/plugins/visualizations/charts/static/charts/others/example/config.js
A config/plugins/visualizations/charts/static/charts/others/example/logo.png
A config/plugins/visualizations/charts/static/charts/others/example/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-parameters.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
M config/plugins/visualizations/charts/static/charts/others/heatmap/wrapper.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/config.js
M config/plugins/visualizations/charts/static/charts/others/heatmap_cluster/wrapper.js
A config/plugins/visualizations/charts/static/charts/overview.js
R config/plugins/visualizations/charts/static/charts/tools.js
M config/plugins/visualizations/charts/static/charts/types.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-datasets.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-form.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-inputs.js
A config/plugins/visualizations/charts/static/charts/utilities/tabular-utilities.js
A config/plugins/visualizations/charts/static/components/jobs.js
A config/plugins/visualizations/charts/static/components/model.js
A config/plugins/visualizations/charts/static/components/screenshot.js
A config/plugins/visualizations/charts/static/components/storage.js
R config/plugins/visualizations/charts/static/library/datasets.js
R config/plugins/visualizations/charts/static/library/jobs.js
R config/plugins/visualizations/charts/static/library/screenshot.js
R config/plugins/visualizations/charts/static/library/storage.js
R config/plugins/visualizations/charts/static/models/chart.js
R config/plugins/visualizations/charts/static/models/config.js
A config/plugins/visualizations/charts/static/views/description.js
M config/plugins/visualizations/charts/static/views/editor.js
M config/plugins/visualizations/charts/static/views/groups.js
M config/plugins/visualizations/charts/static/views/settings.js
M config/plugins/visualizations/charts/static/views/types.js
M config/plugins/visualizations/charts/static/views/viewer.js
M config/plugins/visualizations/charts/static/views/viewport.js
M config/plugins/visualizations/charts/templates/charts.mako
A doc/source/admin/chat-0.png
A doc/source/admin/chat-1.png
A doc/source/admin/chat-2.png
A doc/source/admin/chat-3.png
A doc/source/admin/chat-4.png
A doc/source/admin/chat.rst
A doc/source/admin/communication_server.png
A doc/source/admin/communication_server_rooms.png
A doc/source/admin/conda_faq.rst
M doc/source/admin/index.rst
A doc/source/releases/16.07.rst
M doc/source/releases/16.07_announce.rst
A doc/source/releases/16.10_announce.rst
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/web/framework/base.py
A lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M scripts/bootstrap_history.py
M static/maps/mvc/dataset/data.js.map
M static/maps/mvc/form/form-data.js.map
M static/maps/mvc/form/form-view.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/utils/utils.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/utils/utils.js
R templates/admin/tool_shed_repository/browse_categories.mako
A templates/admin/tool_shed_repository/browse_toolsheds.mako
R templates/admin/tool_shed_repository/preview_repository.mako
M templates/webapps/galaxy/workflow/display.mako
M templates/webapps/tool_shed/index.mako
A test/api/test_api_batch.py
A test/casperjs/api-batch-tests.js
Log Message:
-----------
Merge branch 'dev' into bbi-js3
Commit: 5518c20a20e6fc38ac1edfbbdaa2a8a4f1737c95
https://github.com/galaxyproject/galaxy/commit/5518c20a20e6fc38ac1edfbbdaa2…
Author: jgoecks <jgoecks(a)gwu.edu>
Date: 2016-08-31 (Wed, 31 Aug 2016)
Changed paths:
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Cleanup: (a) remove debugging statements; (b) use Galaxy app; and (c) fix offset issue for LinePainter using floor instead of ceil.
Commit: f553d387a47d0ef1a58a1522c0f437e3b1783a59
https://github.com/galaxyproject/galaxy/commit/f553d387a47d0ef1a58a1522c0f4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-09-15 (Thu, 15 Sep 2016)
Changed paths:
A client/galaxy/scripts/libs/bbi/bigwig.js
A client/galaxy/scripts/libs/bbi/jquery-ajax-native.js
A client/galaxy/scripts/libs/bbi/jszlib.js
A client/galaxy/scripts/libs/bbi/spans.js
A client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
A static/maps/libs/bbi/bigwig.js.map
A static/maps/libs/bbi/jquery-ajax-native.js.map
A static/maps/libs/bbi/jszlib.js.map
A static/maps/libs/bbi/spans.js.map
A static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/tracks.js.map
A static/scripts/libs/bbi/bigwig.js
A static/scripts/libs/bbi/jquery-ajax-native.js
A static/scripts/libs/bbi/jszlib.js
A static/scripts/libs/bbi/spans.js
A static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/trackster/painters.js
M static/scripts/viz/trackster/tracks.js
Log Message:
-----------
Merge pull request #2880 from jgoecks/bbi-js3
Trackster: Read numerical data directly from bigwig files
Compare: https://github.com/galaxyproject/galaxy/compare/921933ea9cb1...f553d387a47d